Highlights d Protein-protein docking by fast Fourier transform (FFT) samples billions of conformations d FFT-based methods need rigid body approximation and scoring by correlation functions d Rigid methods yield more good models in the top 5 predictions than flexible docking d Flexible methods yield higher accuracy models for some targets

When exposed to external stimuli such as heat or light, certain single crystals can acquire momentum and undergo motion. On a molecular scale, the motility of such dynamic single crystals is triggered by a phase transition or chemical reaction without gaseous products, and macroscopically manifests as either slow (reversible or irreversible) deformation, or as rapid, almost instantaneous propulsion of the crystals that is oftentimes accompanied by disintegration. While the elastic energy of the slow reconfiguration processes such as bending, twisting and coiling can be utilized for actuation of other objects, the fast disintegrative processes could be exploited to initiate pressure-sensitive applications. This short review intends to summarize recent developments in the growing research on dynamic crystals, especially aspects of the mechanism of rapid motion of thermosalient and photosalient (leaping) crystals. The collective evidence indicates that these solids are organic-based analogues of the inorganic martensitic materials. While qualitative explanation of the molecular processes that lead to the related dynamic phenomena can be provided, quantification of their kinematics, estimation of the useful work that can be extracted, and prediction of their occurrence are yet to be established. Harnessing the potential of these materials to rapidly and efficiently perform the fundamentally important process of transduction of heat or light into kinetic energy appears as a prospective basis for their application in motion gears and devices.

The thermosalient crystals of terephthalic acid are extraordinarily mechanically compliant and reversibly shape-shift between two forms with different crystal habits. While the transition of form II to form I is spontaneous, the transition of form I to form II is latent and can be triggered by applying local mechanical stress, whereby crystals leap several centimeters in air. This mechanosalient effect (mechanically stimulated motility) is due to sudden release of strain that has accrued in the crystal of form I, which is a metastable structure at ambient conditions. High-speed optical analysis and serial scanning electron microscopy reveal that the mechanical effect is due to rapid reshaping of crystal domains on a millisecond time scale triggered by mechanical stimulation. Mechanically pre-deformed crystals taken over the thermal phase transition exhibit memory effects and partially regain their shape, while cracked, sliced, or otherwise damaged crystals tend to recover their macroscopic integrity by restorative action of intermolecular π-π interactions in a manner which resembles the behavior of shape-memory and self-healing polymers. These observations provide additional evidence that the thermo-/photo-/mechanosalient effects are macroscopic manifestations of martensitic-type transitions in molecular solids.

We present the results for CAPRI Round 46, the third joint CASP‐CAPRI protein assembly prediction challenge. The Round comprised a total of 20 targets including 14 homo‐oligomers and 6 heterocomplexes. Eight of the homo‐oligomer targets and one heterodimer comprised proteins that could be readily modeled using templates from the Protein Data Bank, often available for the full assembly. The remaining 11 targets comprised 5 homodimers, 3 heterodimers, and two higher‐order assemblies. These were more difficult to model, as their prediction mainly involved “ab‐initio” docking of subunit models derived from distantly related templates. A total of ~30 CAPRI groups, including 9 automatic servers, submitted on average ~2000 models per target. About 17 groups participated in the CAPRI scoring rounds, offered for most targets, submitting ~170 models per target. The prediction performance, measured by the fraction of models of acceptable quality or higher submitted across all predictors groups, was very good to excellent for the nine easy targets. Poorer performance was achieved by predictors for the 11 difficult targets, with medium and high quality models submitted for only 3 of these targets. A similar performance “gap” was displayed by scorer groups, highlighting yet again the unmet challenge of modeling the conformational changes of the protein components that occur upon binding or that must be accounted for in template‐based modeling. Our analysis also indicates that residues in binding interfaces were less well predicted in this set of targets than in previous Rounds, providing useful insights for directions of future improvements.

A number of well-established servers perform "free" docking of proteins of known structures. In contrast, template-based docking can start from sequences if structures are available for complexes that are homologous to the target. Based on the results of the CAPRI-CASP structure prediction experiments, template-based methods yield more accurate predictions if good templates can be found, but generally fail without such templates. However, free global docking, or focused docking around even poor quality template-based models, can still generate acceptable docked structures in these cases. Based on the analysis of a benchmark set, free docking of heterodimers yields acceptable or better predictions in the top 10 models for around 40% of structures. However, it is likely that a combination of template-based and free docking methods can perform better for targets that have template structures available. Another way of improving the reliability of predictions is adding experimental information as restraints, an option built into several docking servers.